Re: [gmx-users] cpu/gpu utilization

If you mean [1], then yes I read that and that recommends to use Verlet for the new algorithm depicted in  figures. At least that is my understanding about offloading. If I read the wrong document or you mean there is also some other options, please let me know. [1]

[gmx-users] Parmbsc1 force-field

Hi, I am using the parmbsc1 force-field (http://www.gromacs.org/@api/ deki/files/260/=amber99bsc1.ff.tgz) in GROMACS. I am looking for the original paper where the Na+ and Cl- ion 12-6 Lennard-Jones are coming from, but I am having trouble finding them. The Amber17 manual suggests that this

Re: [gmx-users] Gromacs on CPU runs fine, same calculation crashes on GPU with nonbonded interaction larger than table limit

I was not aware that the way I set it up temperature and pressure from NVT and NPT equilibrations were not taken over. After supplying the checkpoint file to grompp via grompp -t the simulation now runs smoothly. Thanks for your help. -Marc On Thu, Mar 1, 2018 at 4:26 PM, Mark Abraham

Re: [gmx-users] Gromacs on CPU runs fine, same calculation crashes on GPU with nonbonded interaction larger than table limit

Hi, Your temperature before step 0 is effectively zero, so it looks like you ran grompp from a coordinate file with no velocities, and didn't have a checkpoint file available when you started the mdrun, so mdrun guessed that you were OK with no checkpoint file. Thus your equlibration didn't have

Re: [gmx-users] Gromacs on CPU runs fine, same calculation crashes on GPU with nonbonded interaction larger than table limit

Hi Justing, I followed your advice and compiled GROMACS 2016.4 version and used this vanilla version (no Plumed patch applied). I see a very similar behavior as described beofre, in that when starting the simulation on a CPU only node, the system behaves well (simulation is now running for 2ns+

Re: [gmx-users] GROMACS mpirun with extremely high load imbalance in output (vol 0.43! imb F 15- 53%)

Hi, It would be easier to offer an opinion if we knew what was in the simulation system (does load imbalance even make sense?) and what the performance characteristics are without PLUMED. Because of the way PLUMED works, we can make no promises as to performance or correctness... Mark On Thu,

[gmx-users] 2018: large performance variations

Hi,I ran a few MD runs with identical input files (the SAME tpr file. mdp included below) on the same computer with gmx 2018 and observed rather large performance variations (~50%) as in: grep Performance */mcz1.log7/mcz1.log:Performance:   98.510    0.244 7d/mcz1.log:Performance: 

[gmx-users] GROMACS mpirun with extremely high load imbalance in output (vol 0.43! imb F 15- 53%)

Hi gromacs-users, I am currently running a set of TMD simulations with gromacs 5.1.4 + plumed_2.4.0. The system for all four runs is identical, the only difference is the force constant for bias applied by plumed. I am using gromacs with mpi support, starting it with 32 processes on my 32core

Re: [gmx-users] Creating Forcefield without ffbonded.itp

You could do something similar in a Top file. Or make unique names for the parameters to correspond directly the the specific molecule you are interested in. -Micholas === Micholas Dean Smith, PhD. MRSC Post-doctoral Research Associate University of Tennessee/Oak Ridge National

[gmx-users] Creating Forcefield without ffbonded.itp

Hello, is it possible to include all needed bonded parameters (bond lenght, bond angle,...) in the .rtp file and ignore the ffbonded.itp completely? Such case would be if a molecules structure has specified parameters which only fit said structure. According to the manual bond length and

Re: [gmx-users] cpu/gpu utilization

Have you read the "Types of GPU tasks" section of the user guide? -- Szilárd On Thu, Mar 1, 2018 at 3:34 PM, Mahmood Naderan wrote: > >Again, first and foremost, try running PME on the CPU, your 8-core Ryzen > will be plenty fast for that. > > > Since I am a computer guy

Re: [gmx-users] atom naming needs to be considered.

On 3/1/18 9:35 AM, neelam wafa wrote: Hi! Dear all I am running pdb2gmx command to create the protein topology but getting this error. please guide me how to fix this problem. WARNING: WARNING: Residue 1 named TRP of a molecule in the input file was mapped to an entry in the topology

Re: [gmx-users] QM/MM optimization in gromacs/gaussian (nikol...@spbau.ru)

Hi, It is possible, but only using gromacs' internal optizers: SD(steep), CG, or BFGS. And you can only optimise minima, not transition states. Best, Gerrit Message: 3 Date: Thu, 1 Mar 2018 12:44:53 +0300 From: nikol...@spbau.ru To: gmx-us...@gromacs.org Subject: [gmx-users] QM/MM

[gmx-users] atom naming needs to be considered.

Hi! Dear all I am running pdb2gmx command to create the protein topology but getting this error. please guide me how to fix this problem. WARNING: WARNING: Residue 1 named TRP of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of

Re: [gmx-users] cpu/gpu utilization

>Again, first and foremost, try running PME on the CPU, your 8-core Ryzen will >be plenty fast for that. Since I am a computer guy and not a chemist, the question may be noob! What do you mean exactly by running pme on cpu? You mean "-nb cpu"? or you mean setting cut-off to Group instead of

Re: [gmx-users] cpu/gpu utilization

No, that does not seem to help much because the GPU is rather slow at getting the PME Spread done (there's still 12.6% wait for the GPU to finish that), and there are slight overheads that end up hurting performance. Again, first and foremost, try running PME on the CPU, your 8-core Ryzen will be

Re: [gmx-users] cpu/gpu utilization

>- as noted above try offloading only the nonbondeds (or possibly the hybrid >PME mode -pmefft cpu) So, with "-pmefft cpu", I don't see any good impact!See the log at https://pastebin.com/RTYaKSne I will use other options to see the effect. Regards, Mahmood -- Gromacs Users mailing list

[gmx-users] gmx, threads, pinoffset and stride

doing some test runs to optimize the mdrun settings for my hardwarei noticed a couple of things i fail to understand (everything below is gmx-2018on an intel CPU 6 cores, 2 threads each, and GTX 1060) 1) when i start a run as in, e.g.:  prompt> gmx mdrun -v -nt 12 -ntmpi 1 -ntomp 12  -deffnm

Re: [gmx-users] creating topology for ligand

On 3/1/18 8:03 AM, neelam wafa wrote: Dear gmx users I am trying to run a protein ligand simmulation. How can i create topolgy for ligand. prodrg topology is not reliable then which server or software can be used? can topology be created by T LEEP off ambertools package for gromacs?? The

Re: [gmx-users] Pressure using solvation shell

On 2/28/18 3:28 PM, Abramyan, Tigran wrote: Dear Gromacs Users, I am using a solvation shell (-shell command) around a large nucleosome system to accelerate the simulation speed, and was wondering what ensemble is suggested to run such a system in a solvation shell? After a few trial

[gmx-users] creating topology for ligand

Dear gmx users I am trying to run a protein ligand simmulation. How can i create topolgy for ligand. prodrg topology is not reliable then which server or software can be used? can topology be created by T LEEP off ambertools package for gromacs?? secondly how to select the boxtype as I am new to

Re: [gmx-users] cpu/gpu utilization

On Thu, Mar 1, 2018 at 8:25 AM, Mahmood Naderan wrote: > >(try the other parallel modes) > > Do you mean OpenMP and MPI? > No, I meant different offload modes. > > >- as noted above try offloading only the nonbondeds (or possibly the > hybrid PME mode -pmefft cpu) > >

[gmx-users] QM/MM optimization in gromacs/gaussian

Dear all! I need to perform the QM/MM optimization in the Gromacs/Gaussian interface. However, I know that in 2015 this was not possible. The question: is there such an opportunity nowadays (I use gromacs 5.1.2) and which kind of parameters I need to write in the .mdp file in order to obtain